柑橘衰退病毒基因组的简单重复序列分布分析

柑橘衰退病毒（Citrus tristeza virus,CTV）属于长线性病毒科（Closteroviridae）,是目前已知植物病毒中基因组最大的病毒,其引起的柑橘衰退病对全世界的柑橘产业造成着严重影响。本文以在GenBank登录的32条全长CTV基因组序列为材料,分析简单重复序列（Simple Sequence Repeats,SSRs）在其基因组序列中的分布情况。研究结果显示,在所有的CTV基因组中均有SSRs的分布,SSRs重复次数较少,二型SSRs占主导地位,未在CTV基因组序列中发现五型和六型SSRs。在32条基因组全长序列中仅在5条序列中发现四型SSRs。这是首次以柑橘病毒为材料进行的SSRs分析研究。     

In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction

We have developed a website, www.in-silico.com, which runs a software program that performs three basic tasks in completely sequenced bacterial genomes by in silico analysis: PCR amplification, amplified fragment length polymorphism (AFLP-PCR) and endonuclease restriction. For PCR, after selection of the genome and introduction of primers, fragment size, DNA sequence and corresponding open reading frame (ORF) identity of the resulting PCR product is computed. Plasmids of sequenced species may be included in the analysis. Theoretical AFLP-PCR analyzes similar parameters, and includes a suggestion tool providing a list of commercial restriction enzyme pairs yielding up to 50 amplicons in the selected genome. Endonuclease restriction analysis of complete genomes and plasmids calculates the number of restriction sites for endonucleases in a given genome. If the number of fragments is 50 or fewer, pulsed field gel electrophoresis image and restriction maps are illustrated. Other tools that have been included in this site are ORF search by name and DNA to protein translation as well as restriction digestion of user-defined DNA sequences. AVAILABILITY: This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com     

In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships

Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8-14.3% of mitochondrial and 30.5-43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8-86.8% of known mitochondrial genes had at least one microsatellite while this value ranged from 78.6-82.9% among the chloroplast genomes. Dinucleotide repeats were the most abundant in the coding and non-coding regions of the mitochondrial genome while mononucleotides were predominant in chloroplast genomes. Maize harbored more repeats in the mitochondrial genome, which could be due to the larger size of genome. A phylogenetic analysis based on mitochondrial and chloroplast genomic microsatellites revealed that rice and sorghum were closer to each other, while wheat was the farthest and this corroborated with the earlier reported phylogenies based on nuclear genome co-linearity and chloroplast gene-based analysis.     

Predicting polymorphic EST‐SSRs in silico

The public availability of large quantities of gene sequence data provides a valuable resource of the mining of Simple Sequence Repeat (SSR) molecular genetic markers for genetic analysis. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated genes. This study presents the characterization of barley EST‐SSRs and the identification of putative polymorphic SSRs from EST data. Polymorphic SSRs are distinguished from monomorphic SSRs by the representation of varying motif lengths within an alignment of sequence reads. Two measures of confidence are calculated, redundancy of a polymorphism and co‐segregation with accessions. The utility of this method is demonstrated through the discovery of 597 candidate polymorphic SSRs, from a total of 452 642 consensus expressed sequences. PCR amplification primers were designed for the identified SSRs. Ten primer pairs were validated for polymorphism in barley and for transferability across species. Analysis of the polymorphisms in relation to SSR motif, length, position and annotation is discussed.     

In silico prediction of proteins related to xyloglucan fucosyltransferases in Solanaceae genomes

Two independent studies have shown that the cell wall of pollen tubes from tobacco and tomato species contained fucosylated xyloglucan (XyG). These findings are intriguing as many reports have shown that XyG of somatic cells of these species is not fucosylated but instead is arabinosylated. In order to produce fucosylated XyG, plants must express a functional galactoside α-2-fucosyltransferase. Here, using a bioinformatics approach, we show that several candidate genes coding for XyG fucosyltransferases are present in the genome of coffee and several Solanaceae species including tomato, tobacco, potato, eggplant and pepper. BLAST and protein alignments with the 2 well-characterized XyG fucosyltransferases from Arabidopsis thaliana and Pisum sativum revealed that at least 6 proteins from different Solanaceae species and from coffee displayed the 3 conserved motifs required for XyG fucosyltransferase activity.     

The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants

Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and rps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by R. Hagemann     

Inheritance and recombination of mitochondrial genomes in plants, fungi and animals

It is generally assumed that mitochondrial genomes are uniparentally transmitted, homoplasmic and nonrecombining. However, these assumptions draw largely from early studies on animal mitochondrial DNA (mtDNA). In this review, we show that plants, animals and fungi are all characterized by episodes of biparental inheritance, recombination among genetically distinct partners, and selfish elements within the mitochondrial genome, but that the extent of these phenomena may vary substantially across taxa. We argue that occasional biparental mitochondrial transmission may allow organisms to achieve the best of both worlds by facilitating mutational clearance but continuing to restrict the spread of selfish genetic elements. We also show that methodological biases and disproportionately allocated study effort are likely to have influenced current estimates of the extent of biparental inheritance, heteroplasmy and recombination in mitochondrial genomes from different taxa. Despite these complications, there do seem to be discernible similarities and differences in transmission dynamics and likelihood of recombination of mtDNA in plant, animal and fungal taxa that should provide an excellent opportunity for comparative investigation of the evolution of mitochondrial genome dynamics.     

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.     

链霉菌基因组中放线菌型整合性接合元件的识别

【目的】链霉菌染色体重组和外源DNA片段插入是影响其遗传多样性的主要因素。旨在考察放线菌型整合性接合元件(AICE)在链霉菌遗传多样性中所发挥的作用。【方法】基于AICE的特征性模块, 采用隐马尔科夫模型预测链霉菌基因组序列中的AICEs。【结果】在已全测序的12条链霉菌染色体和35个质粒中, 共识别出29个AICEs, 其中12个为首次报道。Streptomyces coelicolor基因组中发现了4个AICEs, 而其近缘的Streptomyces lividans却没有。【结论】AICEs都整合在链霉菌染色体的核心区, 且都具有典型的整合环出、复制和接合转移等核心模块, 这些可自行转移的元件在链霉菌基因组可塑性中扮演了重要角色。     

In silico analysis of Myoglobin in Channa striata

Myoglobin is a cytoplasmic hemoprotein, expressed solely in cardiac myocytes and oxidative skeletal muscle fibers, that reversibly binds O₂ by its heme residue. Myoglobin is an essential oxygen-storage hemoprotein capable of facilitating oxygen transport and modulating nitric oxide homeostasis within cardiac and skeletal myocytes. Functionally, myoglobin is well accepted as an O₂- storage protein in muscle, capable of releasing O₂ during periods of hypoxia or anoxia. There is no evidence available regarding active sites, ligand binding sites, antigenic determinants and the ASA value of myoglobin in Channa striata. We further document the predicted active sites in the structural model with solvent exposed ASA residues. During this study, the model was built by CPH program and validated through PROCHECK, Verify 3D, ERRAT and ProSA for reliability. The active sites were predicted in the model with further ASA analysis of active site residues. The discussed information thus provides the predicted active sites, ligand binding sites, antigenic determinants and ASA values of myoglobin model in Channa striata.     

In silico experimentation with a model of hepatic mitochondrial folate metabolism

Background  

In eukaryotes, folate metabolism is compartmentalized and occurs in both the cytosol and the mitochondria. The function of this compartmentalization and the great changes that occur in the mitochondrial compartment during embryonic development and in rapidly growing cancer cells are gradually becoming understood, though many aspects remain puzzling and controversial.     

Lophotrochozoan mitochondrial genomes

Progress in both molecular techniques and phylogenetic methodshas challenged many of the interpretations of traditional taxonomy.One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships withinthis group and the inclusion of some phyla remain uncertain.While much of this progress in phylogenetic reconstruction hasbeen based on comparing single gene sequences, there are alsohigher order features of genomes, such as the relative orderof genes, that have contributed, and this seems likely to beeven more fruitful in the future. Even though tremendous progressis being made on the sequence determination of whole nucleargenomes, the dataset of choice for genome-level characters formany animals across a broad taxonomic range remains mitochondrialgenomes. We review here what is known about mitochondrial genomesof the lophotrochozoans and how comparisons of some of thesefeatures may be useful in discerning the phylogeny of this group.     

In silico analysis of PHB gene family in maize

Prohibitins (PHBs) are highly conserved proteins in species ranging from prokaryotes to eukaryotes. Plant PHBs have been implicated in various cellular processes including development, senescence and stress responses. Although PHBs have been investigated in several plant species including Arabidopsis and tobacco, no systematic gene family analysis has been carried in maize. In the present study, 16 putative PHB genes have been identified. Analysis of the conserved protein motifs and gene structures has revealed high levels of conservation within the phylogenetic subgroups. Published microarray database showed that most maize PHB genes exhibited different expression levels in different tissues and developmental stages. Cis-elements analysis showed that ZmPHB2 and ZmPHB12 may play important roles in plant development. Taken together, we provide a comprehensive bioinformatics analysis of the PHB gene family in maize genome and our data provide an important foundation for further functional study of this gene family in maize.     

In silico prediction of the peroxisomal proteome in fungi,plants and animals

In an attempt to improve our abilities to predict peroxisomal proteins, we have combined machine-learning techniques for analyzing peroxisomal targeting signals (PTS1) with domain-based cross-species comparisons between eight eukaryotic genomes. Our results indicate that this combined approach has a significantly higher specificity than earlier attempts to predict peroxisomal localization, without a loss in sensitivity. This allowed us to predict 430 peroxisomal proteins that almost completely lack a localization annotation. These proteins can be grouped into 29 families covering most of the known steps in all known peroxisomal pathways. In general, plants have the highest number of predicted peroxisomal proteins, and fungi the smallest number.